|
Status |
Public on Apr 24, 2024 |
Title |
PXGL, ATAC, Rep1 |
Sample type |
SRA |
|
|
Source name |
H9
|
Organism |
Homo sapiens |
Characteristics |
hesc status: Primed cell line: H9 cell type: human embryonic stem cell
|
Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was extracted using the MinElute PCR purification kit (QIAGEN). Transposed DNA were pre-amplified for 5 cycles. The required number of additional cycles for each sample was determined by qPCR as described (Buenrostro et al., 2015). After the final amplification, double-sided bead purification was performed with AMPure XP beads.
|
|
|
Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
ATAC-seq raw data was processed using the atacseq pipeline (v1.2.1) (https://github.com/nf-core/atacseq/) from nf-core using the default parameters Adapter trimming using Trim Galore Reads were aligned using BWA aligner Duplicates were marked by picard bigWig tracks were generated by BEDTools. Assembly: hg38 Supplementary files format and content: bigWig
|
|
|
Submission date |
Oct 31, 2023 |
Last update date |
Apr 24, 2024 |
Contact name |
Claire Rougeulle |
E-mail(s) |
claire.rougeulle@u-paris.fr
|
Organization name |
Université Paris Cité, CNRS
|
Department |
Epigenetics and Cell Fate
|
Street address |
35 rue Helene Brion
|
City |
Paris |
ZIP/Postal code |
75013 |
Country |
France |
|
|
Platform ID |
GPL24676 |
Series (2) |
GSE246633 |
XIST dampens X chromosome activity in a SPEN-dependent manner during early human development [ATAC-seq] |
GSE246643 |
XIST dampens X chromosome activity in a SPEN-dependent manner during early human development |
|
Relations |
BioSample |
SAMN38050701 |
SRA |
SRX22318364 |